1
|
REVILL KATE, WANG TIM, LACHENMAYER ANJA, KOJIMA KENSUKE, HARRINGTON ANDREW, LI JINYU, HOSHIDA YUJIN, LLOVET JOSEPM, POWERS SCOTT. Genome-wide methylation analysis and epigenetic unmasking identify tumor suppressor genes in hepatocellular carcinoma. Gastroenterology 2013; 145:1424-35.e1-25. [PMID: 24012984 PMCID: PMC3892430 DOI: 10.1053/j.gastro.2013.08.055] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/30/2013] [Accepted: 08/29/2013] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Epigenetic silencing of tumor suppressor genes contributes to the pathogenesis of hepatocellular carcinoma (HCC). To identify clinically relevant tumor suppressor genes silenced by DNA methylation in HCC, we integrated DNA methylation data from human primary HCC samples with data on up-regulation of gene expression after epigenetic unmasking. METHODS We performed genome-wide methylation analysis of 71 human HCC samples using the Illumina HumanBeadchip27K array; data were combined with those from microarray analysis of gene re-expression in 4 liver cancer cell lines after their exposure to reagents that reverse DNA methylation (epigenetic unmasking). RESULTS Based on DNA methylation in primary HCC and gene re-expression in cell lines after epigenetic unmasking, we identified 13 candidate tumor suppressor genes. Subsequent validation led us to focus on functionally characterizing 2 candidates, sphingomyelin phosphodiesterase 3 (SMPD3) and neurofilament, heavy polypeptide (NEFH), which we found to behave as tumor suppressor genes in HCC. Overexpression of SMPD3 and NEFH by stable transfection of inducible constructs into an HCC cell line reduced cell proliferation by 50% and 20%, respectively (SMPD3, P = .003 and NEFH, P = .003). Conversely, knocking down expression of these genes with small hairpin RNA promoted cell invasion and migration in vitro (SMPD3, P = .0001 and NEFH, P = .022), and increased their ability to form tumors after subcutaneous injection or orthotopic transplantation into mice, confirming their role as tumor suppressor genes in HCC. Low levels of SMPD3 were associated with early recurrence of HCC after curative surgery in an independent patient cohort (P = .001; hazard ratio = 3.22; 95% confidence interval: 1.6-6.5 in multivariate analysis). CONCLUSIONS Integrative genomic analysis identified SMPD3 and NEFH as tumor suppressor genes in HCC. We provide evidence that SMPD3 is a potent tumor suppressor gene that could affect tumor aggressiveness; a reduced level of SMPD3 is an independent prognostic factor for early recurrence of HCC.
Collapse
Affiliation(s)
- KATE REVILL
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York,Mount Sinai Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - TIM WANG
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York,Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - ANJA LACHENMAYER
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Department of General, Visceral, and Pediatric Surgery, University Hospital Düsseldorf, Düsseldorf, Germany
| | - KENSUKE KOJIMA
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - ANDREW HARRINGTON
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - JINYU LI
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York
| | - YUJIN HOSHIDA
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - JOSEP M. LLOVET
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,HCC Translational Research Laboratory, Barcelona-Clinic Liver Cancer Group, Institut d’Investigacions Biomediques August Pi I Sunyer (IDIBAPS), CIBERehd, Liver Unit, Hospital Clinic, University of Barcelona, Catalonia, Spain,Institucio Catalana de Recerca i Estudis Avancats (ICREA), Catalonia, Spain
| | - SCOTT POWERS
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York
| |
Collapse
|